Dear Erik,
Thanks for your advice. I think you are right. However, when using -pbc whole,
every chain is intact but the three chains separate in some frames; when using
-pbc nojump, the collagen molecule is not intact (there is a small part stay in
the other box ) either. If I fix one end, and
On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:
Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them a
Hi,
If you're planning to use GROMOS parameters set, please take a look at the
following publications, about GROMOS 53A6glyc:
http://pubs.acs.org/doi/pdf/10.1021/ct300479h
http://onlinelibrary.wiley.com/store/10.1002/jcc.23721/asset/jcc23721.pdf;jsessionid=10781A1F0B927C8F5B1C7DB43FB5C856.f04t03?
Thank you, good point.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: Thursday, February 11, 2016 11:58 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1
Hi,
I don't remember, but there are people paid to remember ;-)
Mark
On Thu, 11 Feb 2016 18:53 Irina Kosheleva
wrote:
> Hi Mark,
> Exactly what location I can find them to include, do you know?
> Irina.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [m
Hi Mark,
Exactly what location I can find them to include, do you know?
Irina.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: Thursday, February 11, 2016 11:47 AM
To: gm
No, I'm not sure. As a matter of fact I was not able to find source of
libxml2-devel (+xz-devel, +zlib-devel) (tar.gz) for this arch to install it
as a user. You might be right on this comment.
Thank you.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[ma
Hi,
IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
sure the have/will on Mira too! Ask them.
Mark
On Thu, 11 Feb 2016 18:33 Smith, Micholas D. wrote:
> Quick clarifying question, are you sure you have the development version
> of the libxml2 package (the source wit
Dear All,
I am interested in doing MD simulation on protein and CTP molecule,
preferably in amber99sb-ildn ff in Gromacs. Well, I think we can also use
GAFF for CTP in combination with amber99-sb-ildn for protein. Please
correct me if I am wrong.
There are parameter files for ATP and GTP in .prep
Quick clarifying question, are you sure you have the development version of the
libxml2 package (the source with the headers and everything)?
Also this might be a good time to complain to your sys-admin to install the
libxml2-dev library, as it is used in a lot of other programs too, and you
wo
Dear gmx-users.
I would like to install gromacs-5.1.1 on a cluster where I have only user
privileges. The machine has arch linux-rhel_6-ppc64.
I would like to install it with unittest support thus I need libxml2.a compiled
library.
The cluster does not have this library installed so I have downlo
Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:
[ INN ]
[ atoms ]
Take a look at the CHARMM-GUI input generator - that allows you to set
up simulations for glycans and various glycosylated systems
Krzysztof Kuczera
On 2/11/16 6:59 AM, David Newman wrote:
Hi all,
I'm starting a MD project using gromacs and we're looking to expand on the
previous work in the
You can have a look at few related work:
http://selene.princeton.edu/FFPTM/
http://vienna-ptm.univie.ac.at/
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003154
--
Thanks and Regards,
Bipin Singh
On Thu, Feb 11, 2016 at 6:29 PM, David Newman
Hi all,
I'm starting a MD project using gromacs and we're looking to expand on the
previous work in the lab modelling our receptors of interest by looking at the
effects of gylcosylation. Is there a current best standard for parameters for
modelling glycans?
Thanks,
--
Gromacs Users mailing l
On 2/11/16 7:13 AM, Natalie Stephenson wrote:
Hi all,
I'm experiencing a problem with my trajectory waters. Really early on in the
simulation the waters begin expanding out of the box. There are no system
errors that I am aware of and the simulation runs fine.
Is this something that can be
Hi all,
I'm experiencing a problem with my trajectory waters. Really early on in the
simulation the waters begin expanding out of the box. There are no system
errors that I am aware of and the simulation runs fine.
Is this something that can be fixed with trjconv? Or is it something more
worry
It was very helpful... thanks a lot.
Sent using Boxer
On Feb 11, 2016 2:20 PM, Justin Lemkul wrote:
On 2/11/16 5:28 AM, M S wrote:
> I thought the tutorial set the em parameters lower than nvt parameters based
> on a specific reason. So there is no specific reason in tutorial?
>
No. Gene
Please keep the discussion on the mailing list.
On 2/10/16 10:31 PM, Sana Saeed wrote:
My question is, even if i use Acpype , and follow the steps of making complex
files as in tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
can
I use these fi
Thanks for replying so fast.
Sent using Boxer
On Feb 11, 2016 2:05 PM, Mark Abraham wrote:
Hi,
That's up to the author of the tutorial. Smaller list sizes are faster to
run, and if the purpose of the EM is to ensure that equilibration succeeds,
then anything that works, works.
Mark
On Thu, F
On 2/11/16 5:28 AM, M S wrote:
I thought the tutorial set the em parameters lower than nvt parameters based
on a specific reason. So there is no specific reason in tutorial?
No. Generally I aim to keep them the same throughout, for consistency. In this
case, it's just an oversight, but
Hi,
That's up to the author of the tutorial. Smaller list sizes are faster to
run, and if the purpose of the EM is to ensure that equilibration succeeds,
then anything that works, works.
Mark
On Thu, Feb 11, 2016 at 11:28 AM M S wrote:
> I thought the tutorial set the em parameters lower than
I thought the tutorial set the em parameters lower than nvt parameters based
on a specific reason. So there is no specific reason in tutorial?
Best regards
Sent using Boxer
On Feb 11, 2016 12:22 PM, Mark Abraham wrote:
Hi,
On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr
wrote:
> Dear all us
Dear Ming,
Sounds like a visualisation problem. Does it persist if you e.g. translate the
system with trjconv?
Kind regards,
Erik
> On 11 Feb 2016, at 00:44, Ming Tang wrote:
>
> Dear list,
>
> I am pulling a triple helix using umbrella distance. When the pulling rate is
> 0.0004 nm/ps, the
Hi,
On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr
wrote:
> Dear all users,
>
> In mdp files in ligand tutorial, rvdw,rlist.are equal to 1 in em step,.
> And are equal to 1.4 in nvt,npt and production md
>
> When we can set different interaction parameters for different step?
>
You should choos
Dear all users,
In mdp files in ligand tutorial, rvdw,rlist.are equal to 1 in em step,.
And are equal to 1.4 in nvt,npt and production md
When we can set different interaction parameters for different step?
Best regards
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